Iron in PDB 2cdv: Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution
Protein crystallography data
The structure of Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution, PDB code: 2cdv
was solved by
Y.Higuchi,
M.Kusunoki,
Y.Matsuura,
N.Yasuoka,
M.Kakudo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
N/A /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.900,
68.100,
34.900,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.6 /
n/a
|
Iron Binding Sites:
The binding sites of Iron atom in the Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution
(pdb code 2cdv). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution, PDB code: 2cdv:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2cdv
Go back to
Iron Binding Sites List in 2cdv
Iron binding site 1 out
of 4 in the Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe108
b:6.0
occ:1.00
|
FE
|
A:HEM108
|
0.0
|
6.0
|
1.0
|
NE2
|
A:HIS70
|
1.9
|
3.1
|
1.0
|
NE2
|
A:HIS106
|
1.9
|
9.0
|
1.0
|
NC
|
A:HEM108
|
2.0
|
5.6
|
1.0
|
NB
|
A:HEM108
|
2.0
|
6.5
|
1.0
|
ND
|
A:HEM108
|
2.0
|
5.6
|
1.0
|
NA
|
A:HEM108
|
2.0
|
6.5
|
1.0
|
CE1
|
A:HIS106
|
2.9
|
8.8
|
1.0
|
CE1
|
A:HIS70
|
2.9
|
3.4
|
1.0
|
CD2
|
A:HIS70
|
3.0
|
2.4
|
1.0
|
C4C
|
A:HEM108
|
3.0
|
5.2
|
1.0
|
C1C
|
A:HEM108
|
3.0
|
6.0
|
1.0
|
C4B
|
A:HEM108
|
3.0
|
6.6
|
1.0
|
C1B
|
A:HEM108
|
3.0
|
6.7
|
1.0
|
C1D
|
A:HEM108
|
3.0
|
5.1
|
1.0
|
C4D
|
A:HEM108
|
3.1
|
6.1
|
1.0
|
CD2
|
A:HIS106
|
3.1
|
8.9
|
1.0
|
C4A
|
A:HEM108
|
3.1
|
6.7
|
1.0
|
C1A
|
A:HEM108
|
3.1
|
6.8
|
1.0
|
CHC
|
A:HEM108
|
3.4
|
7.0
|
1.0
|
CHD
|
A:HEM108
|
3.4
|
5.0
|
1.0
|
CHA
|
A:HEM108
|
3.4
|
6.2
|
1.0
|
CHB
|
A:HEM108
|
3.4
|
6.7
|
1.0
|
ND1
|
A:HIS70
|
4.0
|
4.4
|
1.0
|
ND1
|
A:HIS106
|
4.1
|
9.1
|
1.0
|
CG
|
A:HIS70
|
4.1
|
4.1
|
1.0
|
CG
|
A:HIS106
|
4.2
|
8.7
|
1.0
|
C2C
|
A:HEM108
|
4.2
|
5.7
|
1.0
|
C3B
|
A:HEM108
|
4.2
|
6.6
|
1.0
|
C3C
|
A:HEM108
|
4.2
|
6.0
|
1.0
|
C2B
|
A:HEM108
|
4.2
|
6.3
|
1.0
|
C3D
|
A:HEM108
|
4.3
|
5.6
|
1.0
|
C2D
|
A:HEM108
|
4.3
|
5.0
|
1.0
|
C2A
|
A:HEM108
|
4.3
|
7.2
|
1.0
|
C3A
|
A:HEM108
|
4.3
|
7.2
|
1.0
|
CE2
|
A:TYR66
|
5.0
|
9.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 2cdv
Go back to
Iron Binding Sites List in 2cdv
Iron binding site 2 out
of 4 in the Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe109
b:6.7
occ:1.00
|
FE
|
A:HEM109
|
0.0
|
6.7
|
1.0
|
ND
|
A:HEM109
|
2.0
|
7.2
|
1.0
|
NB
|
A:HEM109
|
2.0
|
5.7
|
1.0
|
NC
|
A:HEM109
|
2.0
|
5.5
|
1.0
|
NA
|
A:HEM109
|
2.0
|
5.6
|
1.0
|
NE2
|
A:HIS52
|
2.1
|
6.5
|
1.0
|
NE2
|
A:HIS35
|
2.1
|
3.9
|
1.0
|
CE1
|
A:HIS35
|
3.0
|
3.9
|
1.0
|
C1C
|
A:HEM109
|
3.0
|
5.2
|
1.0
|
C4D
|
A:HEM109
|
3.0
|
8.2
|
1.0
|
CE1
|
A:HIS52
|
3.0
|
7.0
|
1.0
|
C4B
|
A:HEM109
|
3.0
|
5.0
|
1.0
|
C1D
|
A:HEM109
|
3.0
|
7.5
|
1.0
|
C4C
|
A:HEM109
|
3.0
|
5.3
|
1.0
|
C1B
|
A:HEM109
|
3.0
|
5.7
|
1.0
|
C1A
|
A:HEM109
|
3.1
|
5.9
|
1.0
|
CD2
|
A:HIS52
|
3.1
|
6.3
|
1.0
|
C4A
|
A:HEM109
|
3.1
|
5.2
|
1.0
|
CD2
|
A:HIS35
|
3.1
|
4.2
|
1.0
|
CHC
|
A:HEM109
|
3.3
|
5.0
|
1.0
|
CHD
|
A:HEM109
|
3.4
|
6.4
|
1.0
|
CHA
|
A:HEM109
|
3.4
|
6.9
|
1.0
|
CHB
|
A:HEM109
|
3.4
|
4.9
|
1.0
|
ND1
|
A:HIS35
|
4.1
|
4.2
|
1.0
|
ND1
|
A:HIS52
|
4.1
|
6.0
|
1.0
|
CG
|
A:HIS52
|
4.2
|
6.3
|
1.0
|
CG
|
A:HIS35
|
4.2
|
4.0
|
1.0
|
C2D
|
A:HEM109
|
4.2
|
7.9
|
1.0
|
C3D
|
A:HEM109
|
4.2
|
8.4
|
1.0
|
C3B
|
A:HEM109
|
4.2
|
4.9
|
1.0
|
C2B
|
A:HEM109
|
4.2
|
5.2
|
1.0
|
C2C
|
A:HEM109
|
4.2
|
5.0
|
1.0
|
C3C
|
A:HEM109
|
4.3
|
5.2
|
1.0
|
C2A
|
A:HEM109
|
4.3
|
5.8
|
1.0
|
C3A
|
A:HEM109
|
4.3
|
4.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 2cdv
Go back to
Iron Binding Sites List in 2cdv
Iron binding site 3 out
of 4 in the Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe110
b:8.4
occ:1.00
|
FE
|
A:HEM110
|
0.0
|
8.4
|
1.0
|
NE2
|
A:HIS34
|
1.9
|
6.1
|
1.0
|
ND
|
A:HEM110
|
2.0
|
7.5
|
1.0
|
NC
|
A:HEM110
|
2.0
|
7.4
|
1.0
|
NA
|
A:HEM110
|
2.0
|
9.6
|
1.0
|
NB
|
A:HEM110
|
2.0
|
9.4
|
1.0
|
NE2
|
A:HIS22
|
2.0
|
7.0
|
1.0
|
CE1
|
A:HIS34
|
2.9
|
6.6
|
1.0
|
CE1
|
A:HIS22
|
2.9
|
8.0
|
1.0
|
CD2
|
A:HIS34
|
2.9
|
5.8
|
1.0
|
C1D
|
A:HEM110
|
3.0
|
7.3
|
1.0
|
C4D
|
A:HEM110
|
3.0
|
8.1
|
1.0
|
C1C
|
A:HEM110
|
3.0
|
6.9
|
1.0
|
C1A
|
A:HEM110
|
3.0
|
10.9
|
1.0
|
C4B
|
A:HEM110
|
3.0
|
9.4
|
1.0
|
C4A
|
A:HEM110
|
3.0
|
11.5
|
1.0
|
C4C
|
A:HEM110
|
3.1
|
6.8
|
1.0
|
C1B
|
A:HEM110
|
3.1
|
9.8
|
1.0
|
CD2
|
A:HIS22
|
3.1
|
6.8
|
1.0
|
CHC
|
A:HEM110
|
3.4
|
8.0
|
1.0
|
CHD
|
A:HEM110
|
3.4
|
6.6
|
1.0
|
CHA
|
A:HEM110
|
3.4
|
10.0
|
1.0
|
CHB
|
A:HEM110
|
3.4
|
10.5
|
1.0
|
ND1
|
A:HIS34
|
4.0
|
5.2
|
1.0
|
CG
|
A:HIS34
|
4.1
|
6.1
|
1.0
|
ND1
|
A:HIS22
|
4.1
|
7.3
|
1.0
|
CG
|
A:HIS22
|
4.2
|
7.3
|
1.0
|
C2D
|
A:HEM110
|
4.2
|
8.2
|
1.0
|
C3D
|
A:HEM110
|
4.2
|
8.3
|
1.0
|
C2C
|
A:HEM110
|
4.2
|
6.7
|
1.0
|
C3C
|
A:HEM110
|
4.2
|
5.9
|
1.0
|
C2A
|
A:HEM110
|
4.3
|
12.2
|
1.0
|
C3B
|
A:HEM110
|
4.3
|
9.6
|
1.0
|
C2B
|
A:HEM110
|
4.3
|
9.5
|
1.0
|
C3A
|
A:HEM110
|
4.3
|
11.6
|
1.0
|
CD
|
A:PRO5
|
4.6
|
30.4
|
1.0
|
CE2
|
A:PHE20
|
4.7
|
3.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 2cdv
Go back to
Iron Binding Sites List in 2cdv
Iron binding site 4 out
of 4 in the Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe111
b:7.2
occ:1.00
|
FE
|
A:HEM111
|
0.0
|
7.2
|
1.0
|
NE2
|
A:HIS83
|
1.9
|
7.4
|
1.0
|
NC
|
A:HEM111
|
2.0
|
6.6
|
1.0
|
NA
|
A:HEM111
|
2.0
|
7.4
|
1.0
|
NB
|
A:HEM111
|
2.0
|
7.5
|
1.0
|
ND
|
A:HEM111
|
2.0
|
7.5
|
1.0
|
NE2
|
A:HIS25
|
2.1
|
9.8
|
1.0
|
CE1
|
A:HIS83
|
2.8
|
7.8
|
1.0
|
CD2
|
A:HIS25
|
2.9
|
9.2
|
1.0
|
C1B
|
A:HEM111
|
3.0
|
7.2
|
1.0
|
C1D
|
A:HEM111
|
3.0
|
7.1
|
1.0
|
C4D
|
A:HEM111
|
3.0
|
7.7
|
1.0
|
C4C
|
A:HEM111
|
3.0
|
7.3
|
1.0
|
C1A
|
A:HEM111
|
3.0
|
7.0
|
1.0
|
C4A
|
A:HEM111
|
3.0
|
6.7
|
1.0
|
C4B
|
A:HEM111
|
3.0
|
7.3
|
1.0
|
C1C
|
A:HEM111
|
3.0
|
7.5
|
1.0
|
CD2
|
A:HIS83
|
3.1
|
6.7
|
1.0
|
CE1
|
A:HIS25
|
3.3
|
9.8
|
1.0
|
CHB
|
A:HEM111
|
3.4
|
7.3
|
1.0
|
CHA
|
A:HEM111
|
3.4
|
7.2
|
1.0
|
CHC
|
A:HEM111
|
3.4
|
7.1
|
1.0
|
CHD
|
A:HEM111
|
3.4
|
6.6
|
1.0
|
ND1
|
A:HIS83
|
4.0
|
6.1
|
1.0
|
CG
|
A:HIS83
|
4.1
|
6.8
|
1.0
|
CG
|
A:HIS25
|
4.1
|
9.4
|
1.0
|
C3D
|
A:HEM111
|
4.3
|
8.3
|
1.0
|
C3C
|
A:HEM111
|
4.3
|
7.2
|
1.0
|
C2A
|
A:HEM111
|
4.3
|
7.3
|
1.0
|
C3A
|
A:HEM111
|
4.3
|
7.4
|
1.0
|
C2D
|
A:HEM111
|
4.3
|
7.5
|
1.0
|
C2B
|
A:HEM111
|
4.3
|
6.5
|
1.0
|
ND1
|
A:HIS25
|
4.3
|
9.5
|
1.0
|
C2C
|
A:HEM111
|
4.3
|
7.5
|
1.0
|
C3B
|
A:HEM111
|
4.3
|
7.5
|
1.0
|
CE1
|
A:PHE20
|
5.0
|
4.8
|
1.0
|
|
Reference:
Y.Higuchi,
M.Kusunoki,
Y.Matsuura,
N.Yasuoka,
M.Kakudo.
Refined Structure of Cytochrome C3 at 1.8 A Resolution J.Mol.Biol. V. 172 109 1984.
ISSN: ISSN 0022-2836
PubMed: 6319712
DOI: 10.1016/0022-2836(84)90417-0
Page generated: Sat Aug 3 20:12:14 2024
|